Multiple sequence alignment - TraesCS2D01G011200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G011200 chr2D 100.000 7368 0 0 1 7368 5434307 5441674 0.000000e+00 13607.0
1 TraesCS2D01G011200 chr2D 81.512 1574 214 47 4838 6388 584801390 584799871 0.000000e+00 1223.0
2 TraesCS2D01G011200 chr2D 81.633 147 20 5 2381 2527 574823693 574823554 1.680000e-21 115.0
3 TraesCS2D01G011200 chr2D 79.221 154 22 5 2383 2527 528591440 528591288 1.690000e-16 99.0
4 TraesCS2D01G011200 chr2D 77.703 148 26 2 2386 2526 564441039 564441186 4.740000e-12 84.2
5 TraesCS2D01G011200 chr2D 90.909 55 5 0 638 692 443264988 443264934 2.850000e-09 75.0
6 TraesCS2D01G011200 chr2D 80.220 91 18 0 2426 2516 564478947 564479037 1.330000e-07 69.4
7 TraesCS2D01G011200 chr2A 94.944 4292 154 14 1944 6196 4084813 4089080 0.000000e+00 6665.0
8 TraesCS2D01G011200 chr2A 88.848 1919 147 26 1 1872 4082891 4084789 0.000000e+00 2296.0
9 TraesCS2D01G011200 chr2A 81.384 1778 239 48 4634 6388 718937542 718935834 0.000000e+00 1365.0
10 TraesCS2D01G011200 chr2A 95.833 576 22 2 6246 6819 4089079 4089654 0.000000e+00 929.0
11 TraesCS2D01G011200 chr2A 89.583 192 16 3 7058 7249 4090014 4090201 2.660000e-59 241.0
12 TraesCS2D01G011200 chr2B 90.597 2882 151 30 1315 4147 5797276 5800086 0.000000e+00 3711.0
13 TraesCS2D01G011200 chr2B 91.267 2187 133 21 4476 6626 5804971 5807135 0.000000e+00 2928.0
14 TraesCS2D01G011200 chr2B 81.180 1780 240 48 4634 6388 705044940 705043231 0.000000e+00 1343.0
15 TraesCS2D01G011200 chr2B 92.629 407 26 4 6665 7069 5807134 5807538 3.830000e-162 582.0
16 TraesCS2D01G011200 chr2B 84.365 614 53 17 618 1197 5796416 5797020 4.990000e-156 562.0
17 TraesCS2D01G011200 chr2B 80.603 696 81 31 618 1284 6007574 6006904 8.590000e-134 488.0
18 TraesCS2D01G011200 chr2B 90.032 311 30 1 7058 7368 117787238 117787547 1.150000e-107 401.0
19 TraesCS2D01G011200 chr2B 88.103 311 36 1 7058 7368 858916 858607 1.170000e-97 368.0
20 TraesCS2D01G011200 chr2B 77.134 656 79 22 20 616 5793479 5794122 1.540000e-81 315.0
21 TraesCS2D01G011200 chr2B 91.379 174 15 0 7195 7368 5808011 5808184 9.550000e-59 239.0
22 TraesCS2D01G011200 chr2B 87.500 176 22 0 377 552 5796092 5796267 3.490000e-48 204.0
23 TraesCS2D01G011200 chr2B 79.016 305 38 8 20 300 6061845 6061543 1.260000e-42 185.0
24 TraesCS2D01G011200 chr2B 81.579 190 35 0 2152 2341 705047265 705047076 2.750000e-34 158.0
25 TraesCS2D01G011200 chr2B 79.470 151 23 3 2386 2528 202263668 202263518 4.700000e-17 100.0
26 TraesCS2D01G011200 chr2B 81.000 100 16 3 2430 2528 646025079 646025176 7.930000e-10 76.8
27 TraesCS2D01G011200 chrUn 86.634 1025 112 15 3721 4733 314771178 314772189 0.000000e+00 1110.0
28 TraesCS2D01G011200 chrUn 86.634 1025 112 15 3721 4733 356851688 356850677 0.000000e+00 1110.0
29 TraesCS2D01G011200 chrUn 86.537 1025 113 15 3721 4733 356853838 356852827 0.000000e+00 1105.0
30 TraesCS2D01G011200 chrUn 86.460 1034 107 20 3727 4733 11834605 11835632 0.000000e+00 1103.0
31 TraesCS2D01G011200 chrUn 86.020 980 112 15 3721 4688 364655715 364654749 0.000000e+00 1027.0
32 TraesCS2D01G011200 chrUn 87.701 870 73 17 3727 4571 327873485 327872625 0.000000e+00 983.0
33 TraesCS2D01G011200 chrUn 87.701 870 73 17 3727 4571 327882434 327881574 0.000000e+00 983.0
34 TraesCS2D01G011200 chrUn 87.701 870 73 17 3727 4571 446036448 446037308 0.000000e+00 983.0
35 TraesCS2D01G011200 chrUn 87.515 817 70 15 4732 5535 314772269 314773066 0.000000e+00 915.0
36 TraesCS2D01G011200 chrUn 87.167 826 74 15 4732 5544 356850597 356849791 0.000000e+00 909.0
37 TraesCS2D01G011200 chrUn 87.046 826 75 15 4732 5544 356852747 356851941 0.000000e+00 904.0
38 TraesCS2D01G011200 chrUn 86.951 820 72 13 4732 5535 320415090 320415890 0.000000e+00 889.0
39 TraesCS2D01G011200 chrUn 89.150 682 55 9 4875 5544 347954736 347954062 0.000000e+00 832.0
40 TraesCS2D01G011200 chrUn 85.579 527 60 8 4601 5124 470748670 470749183 8.410000e-149 538.0
41 TraesCS2D01G011200 chrUn 84.416 539 51 9 3225 3730 327883062 327882524 3.970000e-137 499.0
42 TraesCS2D01G011200 chrUn 84.045 539 53 9 3225 3730 327874113 327873575 8.590000e-134 488.0
43 TraesCS2D01G011200 chrUn 85.315 429 35 9 3230 3631 320413466 320413893 1.140000e-112 418.0
44 TraesCS2D01G011200 chrUn 85.315 429 35 9 3230 3631 346259540 346259967 1.140000e-112 418.0
45 TraesCS2D01G011200 chrUn 85.082 429 36 9 3230 3631 364656248 364655821 5.320000e-111 412.0
46 TraesCS2D01G011200 chrUn 83.929 448 42 9 3230 3649 11834017 11834462 1.150000e-107 401.0
47 TraesCS2D01G011200 chrUn 85.013 387 31 8 3230 3590 443893188 443893573 1.170000e-97 368.0
48 TraesCS2D01G011200 chrUn 79.673 428 64 14 140 545 474479728 474480154 3.360000e-73 287.0
49 TraesCS2D01G011200 chrUn 86.735 98 10 1 3633 3727 446036258 446036355 1.010000e-18 106.0
50 TraesCS2D01G011200 chr7B 90.997 311 27 1 7058 7368 682925449 682925140 1.140000e-112 418.0
51 TraesCS2D01G011200 chr7B 90.675 311 28 1 7058 7368 729077379 729077688 5.320000e-111 412.0
52 TraesCS2D01G011200 chr7B 90.675 311 28 1 7058 7368 729144901 729145210 5.320000e-111 412.0
53 TraesCS2D01G011200 chr5B 90.354 311 29 1 7058 7368 559152315 559152006 2.470000e-109 407.0
54 TraesCS2D01G011200 chr5B 89.389 311 32 1 7058 7368 571179338 571179029 2.490000e-104 390.0
55 TraesCS2D01G011200 chr5B 89.333 75 8 0 2453 2527 363570346 363570272 2.190000e-15 95.3
56 TraesCS2D01G011200 chr3D 91.772 158 13 0 7058 7215 349670104 349669947 3.460000e-53 220.0
57 TraesCS2D01G011200 chr3B 88.971 136 15 0 7080 7215 448590887 448590752 1.270000e-37 169.0
58 TraesCS2D01G011200 chr3B 95.833 48 2 0 2468 2515 651274151 651274104 2.200000e-10 78.7
59 TraesCS2D01G011200 chr3B 89.831 59 6 0 2468 2526 622406763 622406821 7.930000e-10 76.8
60 TraesCS2D01G011200 chr5D 80.921 152 19 3 2385 2527 257806495 257806645 2.170000e-20 111.0
61 TraesCS2D01G011200 chr4B 89.394 66 7 0 2468 2533 580383159 580383094 4.740000e-12 84.2
62 TraesCS2D01G011200 chr1D 80.645 93 18 0 2435 2527 444878918 444878826 1.030000e-08 73.1
63 TraesCS2D01G011200 chr1D 100.000 30 0 0 663 692 411623999 411624028 1.000000e-03 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G011200 chr2D 5434307 5441674 7367 False 13607.000000 13607 100.000000 1 7368 1 chr2D.!!$F1 7367
1 TraesCS2D01G011200 chr2D 584799871 584801390 1519 True 1223.000000 1223 81.512000 4838 6388 1 chr2D.!!$R4 1550
2 TraesCS2D01G011200 chr2A 4082891 4090201 7310 False 2532.750000 6665 92.302000 1 7249 4 chr2A.!!$F1 7248
3 TraesCS2D01G011200 chr2A 718935834 718937542 1708 True 1365.000000 1365 81.384000 4634 6388 1 chr2A.!!$R1 1754
4 TraesCS2D01G011200 chr2B 5804971 5808184 3213 False 1249.666667 2928 91.758333 4476 7368 3 chr2B.!!$F4 2892
5 TraesCS2D01G011200 chr2B 5793479 5800086 6607 False 1198.000000 3711 84.899000 20 4147 4 chr2B.!!$F3 4127
6 TraesCS2D01G011200 chr2B 705043231 705047265 4034 True 750.500000 1343 81.379500 2152 6388 2 chr2B.!!$R5 4236
7 TraesCS2D01G011200 chr2B 6006904 6007574 670 True 488.000000 488 80.603000 618 1284 1 chr2B.!!$R2 666
8 TraesCS2D01G011200 chrUn 314771178 314773066 1888 False 1012.500000 1110 87.074500 3721 5535 2 chrUn.!!$F6 1814
9 TraesCS2D01G011200 chrUn 356849791 356853838 4047 True 1007.000000 1110 86.846000 3721 5544 4 chrUn.!!$R4 1823
10 TraesCS2D01G011200 chrUn 347954062 347954736 674 True 832.000000 832 89.150000 4875 5544 1 chrUn.!!$R1 669
11 TraesCS2D01G011200 chrUn 11834017 11835632 1615 False 752.000000 1103 85.194500 3230 4733 2 chrUn.!!$F5 1503
12 TraesCS2D01G011200 chrUn 327881574 327883062 1488 True 741.000000 983 86.058500 3225 4571 2 chrUn.!!$R3 1346
13 TraesCS2D01G011200 chrUn 327872625 327874113 1488 True 735.500000 983 85.873000 3225 4571 2 chrUn.!!$R2 1346
14 TraesCS2D01G011200 chrUn 364654749 364656248 1499 True 719.500000 1027 85.551000 3230 4688 2 chrUn.!!$R5 1458
15 TraesCS2D01G011200 chrUn 320413466 320415890 2424 False 653.500000 889 86.133000 3230 5535 2 chrUn.!!$F7 2305
16 TraesCS2D01G011200 chrUn 446036258 446037308 1050 False 544.500000 983 87.218000 3633 4571 2 chrUn.!!$F8 938
17 TraesCS2D01G011200 chrUn 470748670 470749183 513 False 538.000000 538 85.579000 4601 5124 1 chrUn.!!$F3 523

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
308 2658 0.174845 TTACATCAGAACTCGCCCCG 59.825 55.000 0.00 0.0 0.00 5.73 F
564 2971 1.002868 CCATGAGCCGATCATCCCC 60.003 63.158 0.00 0.0 46.01 4.81 F
1351 3985 0.095417 GCAGCCGTTTCTCGACAATC 59.905 55.000 0.00 0.0 42.86 2.67 F
2535 5197 1.137872 CCCACGGATCTCTCCTTTCTG 59.862 57.143 0.00 0.0 39.65 3.02 F
3168 5846 0.531657 CCAGTCAGAGTGAGAGCCAG 59.468 60.000 6.84 0.0 0.00 4.85 F
4427 9396 0.105408 GGCAATGCATCCCCAATCAC 59.895 55.000 7.79 0.0 0.00 3.06 F
5130 10368 0.541863 CGGTGACTAAGAGGCCCATT 59.458 55.000 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 3758 0.107848 ACCAATCCGTTCGATCCCAC 60.108 55.000 0.00 0.00 0.00 4.61 R
1784 4426 0.765510 ACCCAAACTGAGGTCCAGAC 59.234 55.000 0.00 0.00 45.78 3.51 R
2968 5634 0.538287 AGGCCTGAAGTTTGAGGTGC 60.538 55.000 3.11 0.00 33.73 5.01 R
3485 6166 2.042464 GTGGAGTCATGGGCTCAGATA 58.958 52.381 16.24 2.12 34.83 1.98 R
5130 10368 1.227527 CGCATCCATTAGCCGGTCA 60.228 57.895 1.90 0.00 0.00 4.02 R
5922 11181 1.155889 CAGTGCATTGGAGCGTAACA 58.844 50.000 0.32 0.00 37.31 2.41 R
7084 12645 1.134670 AGCCGAACTTCTATCCTGCAC 60.135 52.381 0.00 0.00 0.00 4.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 2429 7.201956 CCCAAATTCGTTTTCCCCATAATATCA 60.202 37.037 0.00 0.00 0.00 2.15
124 2441 5.003804 CCCATAATATCAGGGGTTTTCTCG 58.996 45.833 0.00 0.00 38.98 4.04
194 2520 1.688811 GGTTGACCCCATGTGGCTA 59.311 57.895 0.00 0.00 0.00 3.93
259 2609 3.712187 GTTGCCCAATTTCAAAACTCGA 58.288 40.909 0.00 0.00 0.00 4.04
294 2644 7.466725 CGTTGTGGATTTATGGTCGATTTACAT 60.467 37.037 0.00 0.00 0.00 2.29
295 2645 7.490962 TGTGGATTTATGGTCGATTTACATC 57.509 36.000 0.00 0.00 0.00 3.06
300 2650 8.283291 GGATTTATGGTCGATTTACATCAGAAC 58.717 37.037 0.00 0.00 0.00 3.01
308 2658 0.174845 TTACATCAGAACTCGCCCCG 59.825 55.000 0.00 0.00 0.00 5.73
313 2663 3.441290 AGAACTCGCCCCGACTCG 61.441 66.667 0.00 0.00 0.00 4.18
349 2700 7.173863 TCAAGTAAAGTGTCAAGAATCGAAC 57.826 36.000 0.00 0.00 0.00 3.95
351 2702 5.607477 AGTAAAGTGTCAAGAATCGAACCA 58.393 37.500 0.00 0.00 0.00 3.67
364 2715 2.877866 TCGAACCAGGCCCAAAAATAA 58.122 42.857 0.00 0.00 0.00 1.40
464 2828 3.949113 GGTACCTGAAATTATTTCCCGCA 59.051 43.478 14.22 0.00 38.90 5.69
500 2864 2.108976 GCCGCCGGATCTTCATCA 59.891 61.111 7.68 0.00 0.00 3.07
552 2916 3.683802 ACTGCTTTCTTCTTCCCATGAG 58.316 45.455 0.00 0.00 0.00 2.90
559 2923 1.139654 CTTCTTCCCATGAGCCGATCA 59.860 52.381 0.00 0.00 43.70 2.92
564 2971 1.002868 CCATGAGCCGATCATCCCC 60.003 63.158 0.00 0.00 46.01 4.81
575 2982 3.790437 CATCCCCGCCTCTGCAGT 61.790 66.667 14.67 0.00 37.32 4.40
608 3015 3.813724 CCCCATCCACCTGCCTCC 61.814 72.222 0.00 0.00 0.00 4.30
732 3186 3.958860 CGATCCCCTGCATCCCCC 61.959 72.222 0.00 0.00 0.00 5.40
733 3187 2.778278 GATCCCCTGCATCCCCCA 60.778 66.667 0.00 0.00 0.00 4.96
739 3193 3.350163 CTGCATCCCCCACCCCTT 61.350 66.667 0.00 0.00 0.00 3.95
745 3199 2.490902 GCATCCCCCACCCCTTTTATAG 60.491 54.545 0.00 0.00 0.00 1.31
772 3226 9.209175 GATATATAACGAGGCAATTCTTTCACT 57.791 33.333 0.00 0.00 0.00 3.41
774 3228 6.910536 ATAACGAGGCAATTCTTTCACTAG 57.089 37.500 0.00 0.00 0.00 2.57
775 3229 3.003480 ACGAGGCAATTCTTTCACTAGC 58.997 45.455 0.00 0.00 0.00 3.42
858 3337 2.035961 GCGGTGACCTGATCTAATAGCA 59.964 50.000 0.00 0.00 0.00 3.49
860 3339 4.302455 CGGTGACCTGATCTAATAGCAAG 58.698 47.826 0.00 0.00 0.00 4.01
866 3345 3.008485 CCTGATCTAATAGCAAGACCCCC 59.992 52.174 0.00 0.00 0.00 5.40
946 3425 1.127582 GCAGACAAATCTCACACGCTC 59.872 52.381 0.00 0.00 30.42 5.03
1071 3564 3.437795 GAGACGCCCGACTTCCGA 61.438 66.667 0.00 0.00 41.76 4.55
1140 3636 2.726351 CCCCTTCTCCTCAGTCCGC 61.726 68.421 0.00 0.00 0.00 5.54
1200 3696 1.588861 GTCTGGTAGCTCGAATTTCGC 59.411 52.381 13.86 1.19 40.21 4.70
1212 3708 2.935627 AATTTCGCGGGGGTCGGATC 62.936 60.000 6.13 0.00 39.69 3.36
1225 3721 2.125106 GGATCTGGGTGGTCGTGC 60.125 66.667 0.00 0.00 0.00 5.34
1251 3747 1.152819 CTCCGTCCGGATCTGGGTA 60.153 63.158 20.82 0.00 44.24 3.69
1262 3758 1.807742 GATCTGGGTAGTCGGATCGAG 59.192 57.143 0.00 0.00 39.05 4.04
1282 3778 0.177141 TGGGATCGAACGGATTGGTC 59.823 55.000 0.00 0.00 34.82 4.02
1304 3800 0.837940 ATCGAGGGCTTAGGGTTTCC 59.162 55.000 0.00 0.00 0.00 3.13
1351 3985 0.095417 GCAGCCGTTTCTCGACAATC 59.905 55.000 0.00 0.00 42.86 2.67
1427 4061 3.105283 AGGCTAGGTAGATTGGTTCGTT 58.895 45.455 0.00 0.00 0.00 3.85
1529 4165 4.570930 TGTTACATTTCACGATGTGCCTA 58.429 39.130 0.00 0.00 40.33 3.93
1536 4172 2.683968 TCACGATGTGCCTAAACTGTC 58.316 47.619 0.00 0.00 32.98 3.51
1566 4206 9.214957 CAAATATTTTGGCATGCTTATGATGAT 57.785 29.630 18.92 4.25 0.00 2.45
1595 4235 1.562475 TCGAATTTCCGGGGGATTCTT 59.438 47.619 17.32 0.00 0.00 2.52
1666 4308 1.451567 GAGGGCTTAGGGTTTCGCC 60.452 63.158 0.00 0.00 41.75 5.54
1746 4388 2.432444 CTTAGGGTGTTTGGCGAATCA 58.568 47.619 0.00 0.00 0.00 2.57
1784 4426 4.003788 ACCGGGTTCGTCAGCAGG 62.004 66.667 6.32 4.70 43.43 4.85
1851 4493 8.563123 TCCGTTACATGATGTTTTTGGTAATA 57.437 30.769 2.29 0.00 0.00 0.98
1852 4494 9.011095 TCCGTTACATGATGTTTTTGGTAATAA 57.989 29.630 2.29 0.00 0.00 1.40
1853 4495 9.796120 CCGTTACATGATGTTTTTGGTAATAAT 57.204 29.630 2.29 0.00 0.00 1.28
1870 4512 8.952278 TGGTAATAATGCTGTTTAGTTGGTTAG 58.048 33.333 0.00 0.00 0.00 2.34
1917 4559 4.877378 ATTGCTTCATTTCACCATGTGT 57.123 36.364 0.00 0.00 34.79 3.72
1924 4566 1.511850 TTTCACCATGTGTCTCAGCG 58.488 50.000 0.00 0.00 34.79 5.18
1936 4578 2.991190 TGTCTCAGCGGTTTAACGAATC 59.009 45.455 0.00 0.00 35.47 2.52
1941 4593 5.025986 TCAGCGGTTTAACGAATCTTTTC 57.974 39.130 0.00 0.00 35.47 2.29
1990 4644 5.479306 TGAGACTAGTTTGGTTATGCAGAC 58.521 41.667 0.00 0.00 0.00 3.51
2535 5197 1.137872 CCCACGGATCTCTCCTTTCTG 59.862 57.143 0.00 0.00 39.65 3.02
2744 5410 3.946606 TGATTCTGTGTCATGCTGTCAT 58.053 40.909 0.00 0.00 0.00 3.06
2968 5634 2.503356 AGGCCAACTTCTCAGTCTATGG 59.497 50.000 5.01 0.00 33.14 2.74
3127 5805 2.343758 CGGGTGTCCAGTCTGGTG 59.656 66.667 18.65 0.00 39.03 4.17
3168 5846 0.531657 CCAGTCAGAGTGAGAGCCAG 59.468 60.000 6.84 0.00 0.00 4.85
3266 5944 3.367703 CCAAATTCTCAGCACAATCACCC 60.368 47.826 0.00 0.00 0.00 4.61
3485 6166 4.927267 TCTTACATCCACCATTCAAGGT 57.073 40.909 0.00 0.00 44.48 3.50
3619 6332 9.048446 ACTCAAATCATTGTTTTCCTTTGATTG 57.952 29.630 0.00 0.00 37.17 2.67
3637 6350 6.959671 TGATTGGTTTGTTTTTCACAAGTC 57.040 33.333 0.00 0.00 46.37 3.01
3892 8857 6.073548 GCCATCCTAGTTGAATGACTAAATCG 60.074 42.308 0.00 0.00 32.10 3.34
3893 8858 6.986817 CCATCCTAGTTGAATGACTAAATCGT 59.013 38.462 0.00 0.00 32.10 3.73
4065 9032 3.545703 ACAGAGGTCACTTGTCCTTTTG 58.454 45.455 0.00 2.52 33.78 2.44
4110 9079 0.592637 TGGTTTTGCGCATCTCTGTG 59.407 50.000 12.75 0.00 35.92 3.66
4128 9097 4.080243 TCTGTGACTTAAACCCTTGGTTCA 60.080 41.667 0.00 0.00 46.20 3.18
4178 9147 5.645497 CACTACCTGAAGCAAAAGCTAATCT 59.355 40.000 0.00 0.00 0.00 2.40
4184 9153 7.995488 ACCTGAAGCAAAAGCTAATCTATACAT 59.005 33.333 0.00 0.00 0.00 2.29
4320 9289 3.618351 ACATCATTTCCTGGCTCTTCTG 58.382 45.455 0.00 0.00 0.00 3.02
4427 9396 0.105408 GGCAATGCATCCCCAATCAC 59.895 55.000 7.79 0.00 0.00 3.06
4775 9998 5.491070 ACAGAGCAATGATAACTACTTGCA 58.509 37.500 8.60 0.00 44.90 4.08
5130 10368 0.541863 CGGTGACTAAGAGGCCCATT 59.458 55.000 0.00 0.00 0.00 3.16
5200 10439 6.201425 GTCACAGTTCATGAATTGTTGCAATT 59.799 34.615 28.14 7.79 38.88 2.32
5202 10441 7.924947 TCACAGTTCATGAATTGTTGCAATTAA 59.075 29.630 28.14 1.59 38.88 1.40
5292 10537 8.006590 CGCTACACAGCTCTATTAATTCAATTC 58.993 37.037 0.00 0.00 46.26 2.17
5380 10634 3.138798 GCAGCAGCAGGGTGGATG 61.139 66.667 9.23 0.00 45.14 3.51
5433 10687 0.952280 TCATACAGGGTCGCGATCTC 59.048 55.000 20.42 9.88 0.00 2.75
5536 10793 7.724061 TGAGGTAAACTTTAAGAGGCAGAAAAT 59.276 33.333 0.00 0.00 0.00 1.82
5670 10928 7.062956 TGCAACAGTCTAACATATGTACTTTCG 59.937 37.037 9.21 0.77 0.00 3.46
5738 10996 9.565213 GTTGGAAGAAATCAAATCTATCAACAG 57.435 33.333 12.69 0.00 38.45 3.16
5922 11181 4.281941 TCAGAGTTCAGACACTTGCTACAT 59.718 41.667 0.00 0.00 0.00 2.29
5957 11233 3.636764 TGCACTGACTGTTTCTCTGACTA 59.363 43.478 0.00 0.00 0.00 2.59
6015 11291 1.072965 GTCCCAGCAGATTATCCCAGG 59.927 57.143 0.00 0.00 0.00 4.45
6104 11380 3.946308 TCTACTTCGTACTGCTGATCG 57.054 47.619 0.00 1.94 0.00 3.69
6189 11465 2.124819 CAGCGCCATCTCTGCCTT 60.125 61.111 2.29 0.00 0.00 4.35
6194 11470 2.515523 CCATCTCTGCCTTGGCGG 60.516 66.667 13.96 13.96 0.00 6.13
6195 11471 2.586245 CATCTCTGCCTTGGCGGA 59.414 61.111 20.53 20.53 33.16 5.54
6196 11472 1.147824 CATCTCTGCCTTGGCGGAT 59.852 57.895 21.80 14.13 33.16 4.18
6197 11473 1.147824 ATCTCTGCCTTGGCGGATG 59.852 57.895 21.80 15.73 33.16 3.51
6198 11474 1.630126 ATCTCTGCCTTGGCGGATGT 61.630 55.000 21.80 11.70 33.16 3.06
6199 11475 2.046023 TCTGCCTTGGCGGATGTG 60.046 61.111 18.29 0.00 33.16 3.21
6200 11476 3.136123 CTGCCTTGGCGGATGTGG 61.136 66.667 14.92 0.00 33.16 4.17
6201 11477 3.925630 CTGCCTTGGCGGATGTGGT 62.926 63.158 14.92 0.00 33.16 4.16
6202 11478 3.443045 GCCTTGGCGGATGTGGTG 61.443 66.667 0.00 0.00 33.16 4.17
6203 11479 2.034066 CCTTGGCGGATGTGGTGT 59.966 61.111 0.00 0.00 33.16 4.16
6204 11480 1.603455 CCTTGGCGGATGTGGTGTT 60.603 57.895 0.00 0.00 33.16 3.32
6205 11481 1.586154 CCTTGGCGGATGTGGTGTTC 61.586 60.000 0.00 0.00 33.16 3.18
6206 11482 1.586154 CTTGGCGGATGTGGTGTTCC 61.586 60.000 0.00 0.00 0.00 3.62
6210 11486 2.033448 GGATGTGGTGTTCCGGCA 59.967 61.111 0.00 0.00 36.30 5.69
6211 11487 2.332654 GGATGTGGTGTTCCGGCAC 61.333 63.158 0.00 0.00 38.56 5.01
6226 11502 4.838486 CACGCCCTCGACGCTCTC 62.838 72.222 0.00 0.00 39.41 3.20
6232 11508 3.132139 CTCGACGCTCTCCCGGAA 61.132 66.667 0.73 0.00 0.00 4.30
6233 11509 3.398353 CTCGACGCTCTCCCGGAAC 62.398 68.421 0.73 0.00 0.00 3.62
6234 11510 4.493747 CGACGCTCTCCCGGAACC 62.494 72.222 0.73 0.00 0.00 3.62
6235 11511 4.144703 GACGCTCTCCCGGAACCC 62.145 72.222 0.73 0.00 0.00 4.11
6397 11724 3.609853 TCAGATTTAGGATGCCACACAC 58.390 45.455 0.00 0.00 0.00 3.82
6484 11817 2.026915 TGTCTGTTGATGGTGATCCCTG 60.027 50.000 0.00 0.00 0.00 4.45
6508 11841 8.445275 TGTTGTAGATGATGTAAACTGTTGTT 57.555 30.769 0.00 0.00 38.16 2.83
6555 11906 7.475137 AGAATAGCAGCTTAGGATAAGTAGG 57.525 40.000 0.00 0.00 0.00 3.18
6695 12046 4.072131 AGTTCGTACTTGCATGGTGAATT 58.928 39.130 4.44 0.00 0.00 2.17
6718 12069 4.455533 TGGACTTGAATGAAGTATGTGTGC 59.544 41.667 0.00 0.00 45.48 4.57
6769 12120 7.094592 TGTGTCGGCATCTTAATTTGTTGAATA 60.095 33.333 0.00 0.00 0.00 1.75
6806 12158 6.238374 GGACAAATTACATCTCCCATGTTACG 60.238 42.308 0.00 0.00 33.76 3.18
6845 12197 2.017138 TCACACACTGACAAAAGCGA 57.983 45.000 0.00 0.00 0.00 4.93
6847 12199 0.657840 ACACACTGACAAAAGCGAGC 59.342 50.000 0.00 0.00 0.00 5.03
6854 12206 2.543848 CTGACAAAAGCGAGCAACTGTA 59.456 45.455 0.00 0.00 0.00 2.74
6860 12212 2.751166 AGCGAGCAACTGTAGATGTT 57.249 45.000 0.00 0.00 0.00 2.71
6883 12235 9.065798 TGTTTGTCTGACTGAATGATGAATTAA 57.934 29.630 9.51 0.00 0.00 1.40
6949 12321 6.607198 TGAAATTCTGGTGAAAAGGAGTTTCT 59.393 34.615 0.00 0.00 45.14 2.52
7002 12374 6.039270 CCTTATTTCCGCTGTCAATTTATGGA 59.961 38.462 0.00 0.00 0.00 3.41
7021 12393 8.827832 TTATGGAATTCTGATGAAATTCCACT 57.172 30.769 24.83 17.96 43.67 4.00
7022 12394 7.729124 ATGGAATTCTGATGAAATTCCACTT 57.271 32.000 24.83 12.79 43.67 3.16
7024 12396 7.965718 TGGAATTCTGATGAAATTCCACTTTT 58.034 30.769 20.75 0.00 40.55 2.27
7051 12423 1.202348 GGCGGATGAAAGGGAGTTTTG 59.798 52.381 0.00 0.00 0.00 2.44
7065 12626 4.441356 GGGAGTTTTGTTCATCACTGCAAA 60.441 41.667 0.00 0.00 0.00 3.68
7072 12633 1.985473 TCATCACTGCAAAGCAAGGT 58.015 45.000 0.00 0.00 38.41 3.50
7075 12636 1.032014 TCACTGCAAAGCAAGGTTCC 58.968 50.000 0.00 0.00 38.41 3.62
7076 12637 0.746063 CACTGCAAAGCAAGGTTCCA 59.254 50.000 0.00 0.00 38.41 3.53
7129 12690 2.401766 GGTTCTGCACATGCCCTCG 61.402 63.158 0.49 0.00 41.18 4.63
7156 12717 4.895961 TCTGCATGATGAGAAGATGATCC 58.104 43.478 0.00 0.00 0.00 3.36
7171 12906 2.376109 TGATCCTACCCGAACTGTCTC 58.624 52.381 0.00 0.00 0.00 3.36
7274 13009 1.064296 GAGTCCATCGTGATCGCGT 59.936 57.895 26.40 12.48 36.96 6.01
7296 13031 2.747460 TCCGCAACCTGAGCATGC 60.747 61.111 10.51 10.51 36.74 4.06
7335 13070 1.580942 CCACCGCATCAACCACTTG 59.419 57.895 0.00 0.00 0.00 3.16
7340 13075 1.066908 CCGCATCAACCACTTGTTTGT 59.933 47.619 0.00 0.00 34.00 2.83
7354 13089 0.883370 GTTTGTCTTTCGCCGGGTCT 60.883 55.000 2.18 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.673711 TCGTATATCTTTTTCTGGTCAATTTGG 58.326 33.333 0.00 0.00 0.00 3.28
55 2372 9.440773 CCTACGGTAAACTTTAGGATTAGTTTT 57.559 33.333 5.65 0.00 40.64 2.43
74 2391 3.198417 ACGAATTTGGGATAACCTACGGT 59.802 43.478 0.00 0.00 41.11 4.83
112 2429 5.134661 TGTTACATTTTCGAGAAAACCCCT 58.865 37.500 12.51 0.00 42.32 4.79
124 2441 7.569297 TCTCACGTGTGTTATGTTACATTTTC 58.431 34.615 16.51 0.00 0.00 2.29
187 2513 0.390603 CCCGTTCGATGTTAGCCACA 60.391 55.000 0.00 0.00 40.71 4.17
194 2520 2.182614 CTTTGCGCCCGTTCGATGTT 62.183 55.000 4.18 0.00 0.00 2.71
236 2573 3.453424 GAGTTTTGAAATTGGGCAACGT 58.547 40.909 0.00 0.00 37.60 3.99
238 2575 3.712187 TCGAGTTTTGAAATTGGGCAAC 58.288 40.909 0.00 0.00 0.00 4.17
239 2576 4.599047 ATCGAGTTTTGAAATTGGGCAA 57.401 36.364 0.00 0.00 0.00 4.52
240 2577 4.599047 AATCGAGTTTTGAAATTGGGCA 57.401 36.364 0.00 0.00 0.00 5.36
259 2609 1.253100 AATCCACAACGCGGGAAAAT 58.747 45.000 12.47 0.00 36.62 1.82
294 2644 2.282958 AGTCGGGGCGAGTTCTGA 60.283 61.111 0.00 0.00 35.97 3.27
295 2645 2.182030 GAGTCGGGGCGAGTTCTG 59.818 66.667 0.00 0.00 39.77 3.02
308 2658 4.120589 ACTTGAAACTTGAGTTCCGAGTC 58.879 43.478 0.00 0.00 38.56 3.36
313 2663 7.085052 ACACTTTACTTGAAACTTGAGTTCC 57.915 36.000 0.00 0.00 37.25 3.62
317 2667 7.974675 TCTTGACACTTTACTTGAAACTTGAG 58.025 34.615 0.00 0.00 0.00 3.02
349 2700 6.003326 ACATTTTCTTTATTTTTGGGCCTGG 58.997 36.000 4.53 0.00 0.00 4.45
351 2702 6.486320 CACACATTTTCTTTATTTTTGGGCCT 59.514 34.615 4.53 0.00 0.00 5.19
364 2715 6.469782 AGTTCCAATCACACACATTTTCTT 57.530 33.333 0.00 0.00 0.00 2.52
415 2779 2.845363 TAGTCGGTCCCTTGGTTTTC 57.155 50.000 0.00 0.00 0.00 2.29
484 2848 0.657840 GTTTGATGAAGATCCGGCGG 59.342 55.000 22.51 22.51 0.00 6.13
733 3187 9.210228 CCTCGTTATATATCCTATAAAAGGGGT 57.790 37.037 0.00 0.00 46.55 4.95
745 3199 8.443937 GTGAAAGAATTGCCTCGTTATATATCC 58.556 37.037 0.00 0.00 0.00 2.59
748 3202 9.692749 CTAGTGAAAGAATTGCCTCGTTATATA 57.307 33.333 0.00 0.00 0.00 0.86
750 3204 6.479001 GCTAGTGAAAGAATTGCCTCGTTATA 59.521 38.462 0.00 0.00 0.00 0.98
756 3210 5.665459 TCTAGCTAGTGAAAGAATTGCCTC 58.335 41.667 20.10 0.00 0.00 4.70
866 3345 6.202188 AGAGTATTTATACGCGATTGGTTTGG 59.798 38.462 15.93 0.00 37.99 3.28
867 3346 7.169308 AGAGAGTATTTATACGCGATTGGTTTG 59.831 37.037 15.93 0.00 37.99 2.93
878 3357 6.220579 TCGAACCGAGAGAGTATTTATACG 57.779 41.667 0.00 0.00 38.28 3.06
946 3425 0.842635 CCAGGGAAGAGAAGATGGGG 59.157 60.000 0.00 0.00 0.00 4.96
1071 3564 3.521529 GATACGGCGCATCCTGGCT 62.522 63.158 10.83 0.00 0.00 4.75
1108 3603 2.123033 GGGGGAGGAGAGAGGAGC 60.123 72.222 0.00 0.00 0.00 4.70
1158 3654 4.008933 GATCGGGGCGGGATCAGG 62.009 72.222 10.44 0.00 40.01 3.86
1179 3675 2.876091 CGAAATTCGAGCTACCAGACA 58.124 47.619 10.18 0.00 43.74 3.41
1181 3677 1.797713 CGCGAAATTCGAGCTACCAGA 60.798 52.381 20.38 0.00 43.74 3.86
1235 3731 1.453762 GACTACCCAGATCCGGACGG 61.454 65.000 6.12 8.01 0.00 4.79
1236 3732 1.783031 CGACTACCCAGATCCGGACG 61.783 65.000 6.12 0.00 0.00 4.79
1237 3733 1.453762 CCGACTACCCAGATCCGGAC 61.454 65.000 6.12 0.11 36.00 4.79
1239 3735 0.539901 ATCCGACTACCCAGATCCGG 60.540 60.000 0.00 0.00 35.61 5.14
1251 3747 1.167155 CGATCCCACTCGATCCGACT 61.167 60.000 0.00 0.00 41.12 4.18
1262 3758 0.107848 ACCAATCCGTTCGATCCCAC 60.108 55.000 0.00 0.00 0.00 4.61
1282 3778 2.029666 CCCTAAGCCCTCGATGCG 59.970 66.667 1.88 0.00 0.00 4.73
1304 3800 2.352617 GCAGATAATCAGCCGAGAGAGG 60.353 54.545 0.00 0.00 0.00 3.69
1306 3802 2.035193 GTGCAGATAATCAGCCGAGAGA 59.965 50.000 0.00 0.00 0.00 3.10
1308 3804 2.034878 AGTGCAGATAATCAGCCGAGA 58.965 47.619 0.00 0.00 0.00 4.04
1311 3807 2.543012 CAGAAGTGCAGATAATCAGCCG 59.457 50.000 0.00 0.00 0.00 5.52
1351 3985 2.192608 GAAAGCAGACGCAAGCAGGG 62.193 60.000 0.00 0.00 42.27 4.45
1379 4013 4.651503 ACAGAACCCATCTAGTCGATTCAT 59.348 41.667 0.00 0.00 36.32 2.57
1427 4061 4.023980 CCAGATCAGAACCAGTACTACCA 58.976 47.826 0.00 0.00 0.00 3.25
1529 4165 6.815089 TGCCAAAATATTTGTCAGACAGTTT 58.185 32.000 2.82 2.06 0.00 2.66
1536 4172 7.707464 TCATAAGCATGCCAAAATATTTGTCAG 59.293 33.333 15.66 0.00 31.73 3.51
1566 4206 2.352388 CCGGAAATTCGAGCTACCAAA 58.648 47.619 0.00 0.00 0.00 3.28
1595 4235 3.975591 AGACCCGGACGGAGACCA 61.976 66.667 13.13 0.00 44.03 4.02
1666 4308 4.559704 GCCTACAGATAATCGACCAAGAGG 60.560 50.000 0.00 0.00 42.21 3.69
1668 4310 3.321111 GGCCTACAGATAATCGACCAAGA 59.679 47.826 0.00 0.00 0.00 3.02
1674 4316 5.453339 CCAAGAAAGGCCTACAGATAATCGA 60.453 44.000 5.16 0.00 0.00 3.59
1784 4426 0.765510 ACCCAAACTGAGGTCCAGAC 59.234 55.000 0.00 0.00 45.78 3.51
1851 4493 3.509967 GCCCTAACCAACTAAACAGCATT 59.490 43.478 0.00 0.00 0.00 3.56
1852 4494 3.089284 GCCCTAACCAACTAAACAGCAT 58.911 45.455 0.00 0.00 0.00 3.79
1853 4495 2.107552 AGCCCTAACCAACTAAACAGCA 59.892 45.455 0.00 0.00 0.00 4.41
1870 4512 6.064717 AGATAAATGTATTTGACTGGAGCCC 58.935 40.000 0.27 0.00 0.00 5.19
1917 4559 3.587797 AGATTCGTTAAACCGCTGAGA 57.412 42.857 0.00 0.00 0.00 3.27
1961 4613 9.542462 TGCATAACCAAACTAGTCTCATTATAC 57.458 33.333 0.00 0.00 0.00 1.47
1962 4614 9.764363 CTGCATAACCAAACTAGTCTCATTATA 57.236 33.333 0.00 0.00 0.00 0.98
1963 4615 8.486210 TCTGCATAACCAAACTAGTCTCATTAT 58.514 33.333 0.00 0.00 0.00 1.28
1968 4622 4.870991 GGTCTGCATAACCAAACTAGTCTC 59.129 45.833 12.36 0.00 36.75 3.36
1990 4644 2.416547 CAGCGTAGAACAGTTTCCATGG 59.583 50.000 4.97 4.97 31.28 3.66
2155 4809 3.704566 GGAAATGGGGTTAGGAAACATCC 59.295 47.826 0.00 0.00 37.34 3.51
2479 5140 8.160106 CCAGGACATATTTTTATAGAAGGAGCT 58.840 37.037 0.00 0.00 0.00 4.09
2535 5197 4.245845 TCCTTGCGGTTTCCAATTAAAC 57.754 40.909 0.00 0.00 38.39 2.01
2703 5366 8.915654 AGAATCAAATTAAAAATGTGAGCGAAC 58.084 29.630 0.00 0.00 0.00 3.95
2718 5381 6.430616 TGACAGCATGACACAGAATCAAATTA 59.569 34.615 0.00 0.00 39.69 1.40
2968 5634 0.538287 AGGCCTGAAGTTTGAGGTGC 60.538 55.000 3.11 0.00 33.73 5.01
3168 5846 2.406616 CGGTTGCCTGGCCATGTAC 61.407 63.158 17.53 6.38 0.00 2.90
3266 5944 3.194116 AGCACTATCATTTTGGCCAAGTG 59.806 43.478 21.90 21.90 36.74 3.16
3485 6166 2.042464 GTGGAGTCATGGGCTCAGATA 58.958 52.381 16.24 2.12 34.83 1.98
3597 6307 8.750515 AACCAATCAAAGGAAAACAATGATTT 57.249 26.923 0.00 0.00 38.34 2.17
3619 6332 5.227152 ACAGTGACTTGTGAAAAACAAACC 58.773 37.500 0.00 0.00 44.97 3.27
3667 6380 8.598916 TCCTCGAGATCATATTCTCTAGTACTT 58.401 37.037 15.71 0.00 40.03 2.24
3892 8857 3.067106 ACCATCGACAACTCATCAACAC 58.933 45.455 0.00 0.00 0.00 3.32
3893 8858 3.401033 ACCATCGACAACTCATCAACA 57.599 42.857 0.00 0.00 0.00 3.33
4065 9032 8.604640 TCAATGAATGAAGAATCATCTCTAGC 57.395 34.615 0.00 0.00 45.60 3.42
4110 9079 5.183331 GGAGATTGAACCAAGGGTTTAAGTC 59.817 44.000 10.49 9.24 46.95 3.01
4178 9147 7.494298 TCTTGAAATCTGCTTTGCGTATGTATA 59.506 33.333 0.00 0.00 0.00 1.47
4184 9153 5.431420 TTTCTTGAAATCTGCTTTGCGTA 57.569 34.783 0.00 0.00 0.00 4.42
4320 9289 4.440663 GCATGGCAAGTTTTATTCCTCTCC 60.441 45.833 0.00 0.00 0.00 3.71
4427 9396 4.895668 TTTACCTACCTTGTACCACCAG 57.104 45.455 0.00 0.00 0.00 4.00
4701 9760 1.586028 TTGCCTCGGCTGCAAAATC 59.414 52.632 9.65 0.00 45.11 2.17
4986 10224 1.872952 GAACCATTTGCTTTTGGTGGC 59.127 47.619 5.91 0.00 45.44 5.01
5021 10259 3.243334 GGCTGGTACTATCGGTTCAGTAC 60.243 52.174 0.82 0.82 44.16 2.73
5130 10368 1.227527 CGCATCCATTAGCCGGTCA 60.228 57.895 1.90 0.00 0.00 4.02
5202 10441 9.672673 AAATAAGCACAGAACTGTCAGTATAAT 57.327 29.630 5.77 0.00 42.83 1.28
5272 10517 7.275920 AGACCGAATTGAATTAATAGAGCTGT 58.724 34.615 0.00 0.00 0.00 4.40
5280 10525 7.415653 GCTGAGGAAAGACCGAATTGAATTAAT 60.416 37.037 0.00 0.00 44.74 1.40
5292 10537 1.649664 CTCATGCTGAGGAAAGACCG 58.350 55.000 5.54 0.00 40.71 4.79
5380 10634 7.295201 TCGCTTCATTTTGTTCACAGTATTAC 58.705 34.615 0.00 0.00 0.00 1.89
5433 10687 1.656652 CTTCCCAGCGGTAGTGATTG 58.343 55.000 0.00 0.00 0.00 2.67
5575 10832 6.372659 TGAGAACAGATAGCACTGGATTTTTC 59.627 38.462 9.61 4.90 41.59 2.29
5686 10944 4.061596 GCCTCATTACTAGCATTCTGTCC 58.938 47.826 0.00 0.00 0.00 4.02
5922 11181 1.155889 CAGTGCATTGGAGCGTAACA 58.844 50.000 0.32 0.00 37.31 2.41
5957 11233 4.558095 GCAAGACAAGACACTGCATCAATT 60.558 41.667 0.00 0.00 0.00 2.32
6104 11380 2.808543 GGCGGATTTGGACATATCTGAC 59.191 50.000 13.49 8.30 29.96 3.51
6189 11465 2.033448 GGAACACCACATCCGCCA 59.967 61.111 0.00 0.00 0.00 5.69
6194 11470 2.677003 CGTGCCGGAACACCACATC 61.677 63.158 14.51 0.00 37.25 3.06
6195 11471 2.668212 CGTGCCGGAACACCACAT 60.668 61.111 14.51 0.00 37.25 3.21
6209 11485 4.838486 GAGAGCGTCGAGGGCGTG 62.838 72.222 7.31 0.00 38.98 5.34
6215 11491 3.132139 TTCCGGGAGAGCGTCGAG 61.132 66.667 0.00 0.00 0.00 4.04
6216 11492 3.437795 GTTCCGGGAGAGCGTCGA 61.438 66.667 0.00 0.00 0.00 4.20
6217 11493 4.493747 GGTTCCGGGAGAGCGTCG 62.494 72.222 0.00 0.00 0.00 5.12
6218 11494 4.144703 GGGTTCCGGGAGAGCGTC 62.145 72.222 0.00 0.00 0.00 5.19
6229 11505 3.135056 CTCGATCGACCGGGGTTCC 62.135 68.421 15.15 0.00 0.00 3.62
6230 11506 2.412112 CTCGATCGACCGGGGTTC 59.588 66.667 15.15 0.86 0.00 3.62
6231 11507 3.145551 CCTCGATCGACCGGGGTT 61.146 66.667 10.99 0.00 44.82 4.11
6235 11511 3.661131 ATCGCCTCGATCGACCGG 61.661 66.667 24.49 21.10 43.45 5.28
6236 11512 2.427575 CATCGCCTCGATCGACCG 60.428 66.667 15.15 18.89 45.19 4.79
6237 11513 2.049985 CCATCGCCTCGATCGACC 60.050 66.667 15.15 7.33 45.19 4.79
6238 11514 2.731348 GCCATCGCCTCGATCGAC 60.731 66.667 15.15 4.53 45.19 4.20
6370 11697 4.458295 GTGGCATCCTAAATCTGATCCATG 59.542 45.833 0.00 0.00 0.00 3.66
6397 11724 2.687935 ACTACAACAAACAAGCCACAGG 59.312 45.455 0.00 0.00 0.00 4.00
6484 11817 9.730420 AAAACAACAGTTTACATCATCTACAAC 57.270 29.630 0.00 0.00 34.53 3.32
6508 11841 8.575649 TCTACATCTATCTCACACAGTACAAA 57.424 34.615 0.00 0.00 0.00 2.83
6555 11906 4.620567 CGAATTCCAAACAGAATTTCCCCC 60.621 45.833 0.00 0.00 44.52 5.40
6640 11991 5.806654 ACCACAAGTAAATTGCAGGATTT 57.193 34.783 2.16 2.16 43.15 2.17
6682 12033 3.229293 TCAAGTCCAATTCACCATGCAA 58.771 40.909 0.00 0.00 0.00 4.08
6695 12046 4.455533 GCACACATACTTCATTCAAGTCCA 59.544 41.667 0.00 0.00 42.07 4.02
6769 12120 6.612247 TGTAATTTGTCCGAATGCGAATAT 57.388 33.333 0.00 0.00 40.82 1.28
6806 12158 1.668419 AAAGACACAGCACAGTGACC 58.332 50.000 4.15 0.00 42.05 4.02
6834 12186 1.378531 ACAGTTGCTCGCTTTTGTCA 58.621 45.000 0.00 0.00 0.00 3.58
6845 12197 4.752101 GTCAGACAAACATCTACAGTTGCT 59.248 41.667 0.00 0.00 0.00 3.91
6847 12199 5.985530 TCAGTCAGACAAACATCTACAGTTG 59.014 40.000 2.66 0.00 0.00 3.16
6854 12206 6.470278 TCATCATTCAGTCAGACAAACATCT 58.530 36.000 2.66 0.00 0.00 2.90
6883 12235 5.667626 TCACCCTTCCAGCTAGAAATAGAAT 59.332 40.000 0.00 0.00 0.00 2.40
6885 12237 4.620723 TCACCCTTCCAGCTAGAAATAGA 58.379 43.478 0.00 0.00 0.00 1.98
6888 12240 3.308473 GGTTCACCCTTCCAGCTAGAAAT 60.308 47.826 0.00 0.00 0.00 2.17
6932 12285 5.751586 ACAGTTAGAAACTCCTTTTCACCA 58.248 37.500 0.00 0.00 45.50 4.17
6949 12321 3.961480 ACAGCAGCACATCTACAGTTA 57.039 42.857 0.00 0.00 0.00 2.24
7051 12423 2.035066 ACCTTGCTTTGCAGTGATGAAC 59.965 45.455 0.00 0.00 40.61 3.18
7072 12633 2.429930 CTGCACGGAGGGTTGGAA 59.570 61.111 0.00 0.00 0.00 3.53
7084 12645 1.134670 AGCCGAACTTCTATCCTGCAC 60.135 52.381 0.00 0.00 0.00 4.57
7129 12690 4.134379 TCTTCTCATCATGCAGAGAACC 57.866 45.455 19.42 0.00 43.74 3.62
7156 12717 0.179161 CTGCGAGACAGTTCGGGTAG 60.179 60.000 0.00 0.00 41.86 3.18
7171 12906 2.628106 CGCCGGAATGATTCTGCG 59.372 61.111 21.11 21.11 41.54 5.18
7193 12928 3.508840 GCGCTTCCACCGGAATGG 61.509 66.667 9.46 6.61 41.23 3.16
7195 12930 2.436646 CTGCGCTTCCACCGGAAT 60.437 61.111 9.46 0.00 41.23 3.01
7216 12951 1.459592 CAAACTCAACGTCGATGGGTC 59.540 52.381 8.60 0.00 29.25 4.46
7218 12953 0.796312 CCAAACTCAACGTCGATGGG 59.204 55.000 9.90 0.11 0.00 4.00
7221 12956 1.069513 TGGACCAAACTCAACGTCGAT 59.930 47.619 0.00 0.00 0.00 3.59
7256 12991 0.930742 GACGCGATCACGATGGACTC 60.931 60.000 15.93 0.00 42.66 3.36
7274 13009 2.962569 CTCAGGTTGCGGACGAGA 59.037 61.111 0.00 0.00 0.00 4.04
7296 13031 2.100631 CCGAGCAAAGCCTGTACCG 61.101 63.158 0.00 0.00 0.00 4.02
7335 13070 0.883370 AGACCCGGCGAAAGACAAAC 60.883 55.000 9.30 0.00 41.50 2.93
7340 13075 3.621805 TGCAGACCCGGCGAAAGA 61.622 61.111 9.30 0.00 0.00 2.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.